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- PDB-5xjw: Crystal Structure of the [Co2+-(Chromomycin A3)2]-CCG repeats Complex -

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Entry
Database: PDB / ID: 5xjw
TitleCrystal Structure of the [Co2+-(Chromomycin A3)2]-CCG repeats Complex
ComponentsDNA (5'-D(*TP*TP*CP*GP*CP*CP*GP*CP*CP*GP*AP*A)-3')
KeywordsDNA/ANTIBIOTIC / Nucleotide Flipping-out / CCG trinucleotide repeats / Chromomycin A3 / Metalloantibiotics / Minor Groove Binding drug / DNA-ANTIBIOTIC complex
Function / homologyChromomycin A3, Monomer / : / Chem-CPH / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.097 Å
AuthorsTseng, W.H. / Wu, P.C. / Satange, R.B. / Hou, M.H.
CitationJournal: To be published
Title: Crystal Structure of the [Co2+-(Chromomycin A3)2]-CCG repeats Complex
Authors: Tseng, W.H. / Wu, P.C. / Satange, R.B. / Hou, M.H.
History
DepositionMay 4, 2017Deposition site: PDBJ / Processing site: PDBJ
SupersessionMay 16, 2018ID: 5ES0
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 2.0Jun 6, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_molecule / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_molecule.prd_id / _pdbx_molecule_features.class / _pdbx_molecule_features.name / _pdbx_molecule_features.prd_id / _pdbx_molecule_features.type / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1Sep 12, 2018Group: Data collection / Structure summary / Category: pdbx_molecule
Revision 2.2Oct 3, 2018Group: Data collection / Structure summary / Category: pdbx_molecule
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*TP*TP*CP*GP*CP*CP*GP*CP*CP*GP*AP*A)-3')
B: DNA (5'-D(*TP*TP*CP*GP*CP*CP*GP*CP*CP*GP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,44011
Polymers7,8252
Non-polymers2,6159
Water90150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.309, 48.309, 83.636
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11B-221-

HOH

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Components

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DNA chain , 1 types, 2 molecules AB

#1: DNA chain DNA (5'-D(*TP*TP*CP*GP*CP*CP*GP*CP*CP*GP*AP*A)-3')


Mass: 3912.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Sugars , 2 types, 4 molecules

#2: Polysaccharide 3-C-methyl-4-O-acetyl-alpha-L-Olivopyranose-(1-3)-beta-D-Olivopyranose-(1-3)-beta-D-Olivopyranose


Type: oligosaccharide, Oligosaccharide / Class: Antibiotic / Mass: 464.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
References: Chromomycin A3, Monomer
DescriptorTypeProgram
WURCS=2.0/2,3,2/[ad122m-1b_1-5][ad611m-1a_1-5_3*C_4*OCC/3=O]/1-1-2/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-2,6-deoxy-Glcp]{[(3+1)][b-D-2,6-deoxy-Glcp]{[(3+1)][a-L-2,6-deoxy-Glcp4Ac]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2,6-dideoxy-4-O-methyl-alpha-D-galactopyranose-(1-3)-4-O-acetyl-2,6-dideoxy-beta-D-galactopyranose


Type: oligosaccharide, Oligosaccharide / Class: Antibiotic / Mass: 334.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
References: Chromomycin A3, Monomer
DescriptorTypeProgram
WURCS=2.0/2,2,1/[ad112m-1b_1-5_4*OCC/3=O][ad112m-1a_1-5_4*OC]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-2-deoxy-Fucp4Ac]{[(3+1)][a-D-2-deoxy-Fucp4Me]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 55 molecules

#4: Chemical ChemComp-CPH / (1S)-5-deoxy-1-O-methyl-1-C-[(2R,3S)-3,5,7,10-tetrahydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen-2-yl]-D-xylulose / None


Type: Oligosaccharide / Class: Antibiotic / Mass: 420.410 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H24O9 / References: Chromomycin A3, Monomer
#5: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.89 Å3/Da / Density % sol: 68.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.0 mM ssDNA, 2.0 mM Chromomycin A3, 4mM CoCl2.6H2O, 50 mM Sodium Cacodylate, 5 mM Spermine, 3% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1.56418 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.56418 Å / Relative weight: 1
ReflectionResolution: 2.097→30 Å / Num. obs: 12596 / % possible obs: 99.6 % / Redundancy: 6.1 % / Biso Wilson estimate: 47.68 Å2 / Rmerge(I) obs: 0.055 / Χ2: 1.887 / Net I/σ(I): 24.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
2.1-2.184.20.2670.961197.8
2.18-2.265.80.2491.0631100
2.26-2.376.40.1851.2341100
2.37-2.496.40.1371.2171100
2.49-2.656.50.1211.2891100
2.65-2.856.50.1011.7921100
2.85-3.146.40.0691.9551100
3.14-3.596.10.0542.1211100
3.59-4.526.20.0472.346199.7
4.52-3060.0484.416198.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
HKL-2000data processing
SCALEPACKdata scaling
PHENIX1.10.1-2155model building
PHENIX1.10.1-2155refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XEW

5xew


Resolution: 2.097→29.576 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.07
Details: The force field of Chro unit used in the refinement of CoII(Chro)2-DNA complex structure was generated using the atomic resolution crystal structure of NiII(Chro)2.
RfactorNum. reflection% reflection
Rfree0.2457 1230 9.77 %
Rwork0.2253 --
obs0.2275 12596 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 123.08 Å2 / Biso mean: 55.6101 Å2 / Biso min: 30.93 Å2
Refinement stepCycle: final / Resolution: 2.097→29.576 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 480 169 50 699
Biso mean--43.95 57.27 -
Num. residues----24
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004714
X-RAY DIFFRACTIONf_angle_d0.7641056
X-RAY DIFFRACTIONf_chiral_restr0.039136
X-RAY DIFFRACTIONf_plane_restr0.00430
X-RAY DIFFRACTIONf_dihedral_angle_d28.767316
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0967-2.18060.34291230.281155127892
2.1806-2.27980.38641450.28781312145799
2.2798-2.40.30771400.300512461386100
2.4-2.55030.29341320.28971271140399
2.5503-2.7470.39331400.296312861426100
2.747-3.02320.28151320.316512971429100
3.0232-3.46010.22171400.20291275141599
3.4601-4.35720.23961340.20241260139499
4.3572-29.57940.19461440.18661264140898

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